Haplotype-tagged SNPs improve genomic prediction accuracy for Fusarium head blight resistance and yield-related traits in wheat

Genomic prediction is a powerful tool to enhance genetic gain in plant breeding. However, the method is accompanied by various complications leading to low prediction accuracy. One of the major challenges arises from the complex dimensionality of marker data. To overcome this issue, we applied two pre-selection methods for SNP markers viz. LD-based haplotype-tagging and GWAS-based trait-linked marker identification. Six different models were tested with preselected SNPs to predict the genomic estimated breeding values (GEBVs) of four traits measured in 419 winter wheat genotypes. Ten different sets of haplotype-tagged SNPs were selected by adjusting the level of LD thresholds. In addition, various sets of trait-linked SNPs were identified with different scenarios from the training-test combined and only from the training populations. The BRR and RR-BLUP models developed from haplotype-tagged SNPs had a higher prediction accuracy for FHB and SPW by 0.07 and 0.092, respectively, compared to the corresponding models developed without marker pre-selection. The highest prediction accuracy for SPW and FHB was achieved with tagged SNPs pruned at weak LD thresholds (r

New DArT markers for oat provide enhanced map coverage and global germplasm characterization

BACKGROUND: Genomic discovery in oat and its application to oat improvement have been hindered by a lack of genetic markers common to different genetic maps, and by the difficulty of conducting whole-genome analysis using high-throughput markers. This study was intended to develop, characterize, and apply a large set of oat genetic markers based on Diversity Array Technology (DArT). RESULTS: Approximately 19,000 genomic clones were isolated from complexity-reduced genomic representations of pooled DNA samples from 60 oat varieties of global origin. These were screened on three discovery arrays, with more than 2000 polymorphic markers being identified for use in this study, and approximately 2700 potentially polymorphic markers being identified for use in future studies. DNA sequence was obtained for 2573 clones and assembled into a non-redundant set of 1770 contigs and singletons. Of these, 705 showed highly significant (Expectation < 10E-10) BLAST similarity to gene sequences in public databases. Based on marker scores in 80 recombinant inbred lines, 1010 new DArT markers were used to saturate and improve the 'Kanota' × 'Ogle' genetic map. DArT markers provided map coverage approximately equivalent to existing markers. After binning markers from similar clones, as well as those with 99% scoring similarity, a set of 1295 non-redundant markers was used to analyze genetic diversity in 182 accessions of cultivated oat of worldwide origin. Results of this analysis confirmed that major clusters of oat diversity are related to spring vs. winter type, and to the presence of major breeding programs within geographical regions. Secondary clusters revealed groups that were often related to known pedigree structure. CONCLUSION: These markers will provide a solid basis for future efforts in genomic discovery, comparative mapping, and the generation of an oat consensus map. They will also provide new opportunities for directed breeding of superior oat varieties, and guidance in the maintenance of oat genetic diversity

The mosaic oat genome gives insights into a uniquely healthy cereal crop

Cultivated oat (Avena sativa L.) is an allohexaploid (AACCDD, 2n = 6x = 42) thought to have been domesticated more than 3,000 years ago while growing as a weed in wheat, emmer and barley fields in Anatolia1,2. Oat has a low carbon footprint, substantial health benefits and the potential to replace animal-based food products. However, the lack of a fully annotated reference genome has hampered efforts to deconvolute its complex evolutionary history and functional gene dynamics. Here we present a high-quality reference genome of A. sativa and close relatives of its diploid (Avena longiglumis, AA, 2n = 14) and tetraploid (Avena insularis, CCDD, 2n = 4x = 28) progenitors. We reveal the mosaic structure of the oat genome, trace large-scale genomic reorganizations in the polyploidization history of oat and illustrate a breeding barrier associated with the genome architecture of oat. We showcase detailed analyses of gene families implicated in human health and nutrition, which adds to the evidence supporting oat safety in gluten-free diets, and we perform mapping-by-sequencing of an agronomic trait related to water-use efficiency. This resource for the Avena genus will help to leverage knowledge from other cereal genomes, improve understanding of basic oat biology and accelerate genomics-assisted breeding and reanalysis of quantitative trait studies

Genetic and environmental factors affecting reproductive variation in Allium vineale

Traits related to allocation of resources to sexual and asexual reproduction, together with seed production, were-scored on Allium vineale plants sampled from five sites in southern Sweden during a period of 4 years. In addition, random amplified polymorphic DNA (RAPD) fingerprinting of the sampled plants allowed the identification of genets. Integration of genetic and phenotypic data from field and greenhouse provided for the analysis of among-year, among-site, and among-genet variance components. These variance components were taken to represent the influences of short-term environmental changes, persistent site divergence, and within-site genet differences, respectively. It was shown that differences among sites and among genets explained a large part of the phenotypic variation of allocation traits, whereas among-year differences had a larger influence on the variation in seed production. Together, the results support the conclusions of a recent model on the evolution of mixed reproductive systems, that predicts a stable balance between sexual and asexual reproduction because of annual fluctuations in fecundity through the two modes

Coalescence times and the Meselson effect in asexual eukaryotes

In asexual eukaryotes, the two allelic gene copies at a locus are expected to become highly divergent as a result of the independent accumulation of mutations in the absence of segregation. If sexual reproduction was abandoned millions of generations ago, intra-individual allelic divergences can be significantly larger than in species that reproduce sexually. Owing to the disputed existence of truly ancient asexual species, this so-called 'Meselson effect' has been put forward as a means of confirming the complete loss of sexual reproduction. Very few attempts have, however, been made at quantifying the effect of sexual reproduction on the degree of divergence between gene copies in an asexual population. Here, I describe how asexual reproduction can be regarded as a special case of population subdivision. Using a slightly modified version of the standard two-deme structured coalescent, I derive the expected coalescence time for a pair of gene copies in an asexual population and show that the Meselson effect is compatible with low rates of sexual reproduction

The importance of sexual and asexual reproduction in the recent evolution of Allium vineale

In the weedy plant species Allium vineale (wild garlic), individuals may simultaneously produce sexually and asexually derived offspring, by seed and bulbils, respectively. In this study, genetic and genotypic diversity was determined in samples from 14 European A. vineale populations using nuclear (RAPD) and cytoplasmic (PCR-RFLP of cpDNA) markers to investigate the importance of the different reproductive modes. In the whole sample, 77 nuclear multilocus genotypes and four chloroplast haplotypes (chlorotypes) were found. Populations exhibited a high degree of subdivision for nuclear and cytoplasmic markers as estimated from hierarchical F-statistics; at the same time, identical chlorotypes could be found in populations separated by large distances. Genotypic diversity was significantly lower than expected under free recombination in almost all populations, indicating that recruitment into populations is mostly by asexually produced offspring. Nevertheless. within each chlorotype, the distribution of markers from pairs of nuclear loci was incompatible with a purely clonal structure, suggesting that many multilocus genotypes have originated by sexual recombination rather than by mutation within asexual lineages. It is argued that the weedy habit of A. vineale is likely to have favored bulbil reproduction, whereas sexually generated genotypes may have facilitated local adaptation during the species' expansion across Europe

The balance between sex and asex: evolutionary genetic studies of reproductive variation in Allium vineale

Evolutionary theory predicts a disadvantage to sexual reproduction. This manifests itself either by the higher growth rate of asexual females in a dioecious species, or by the higher transmission rate of a gene conferring asexual female function to its carriers in a hermaphrodite species. The disadvantage to sexual reproduction may be as high as two-fold provided all else is equal. This phenomenon is known as the 'two-fold cost of sex'. Since most higher organisms nevertheless rely on sexual reproduction, it has been presumed that sex has some advantage that outweighs its cost. However, despite much effort to identify such an advantage, no single hypothesis has received unequivocal empirical support. Moreover, most theories have largely ignored situations in which there is within-population genetic variation for the balance between sexual and asexual reproduction. Also, experimental studies have yet to determine to what extent genetic variation for the degree of sexuality and asexuality exists in natural populations, and the importance of the two reproductive modes in partly asexual organisms. The fact that most organisms capable of asexual reproduction simultaneously retain sexual capacity underscores the importance of these issues for understanding the evolutionary significance of sex. This thesis addresses some of these questions. A theoretical model was set up from which it was concluded that the maintenance of a genetically determined polymorphism for the proportion of sexually produced offspring is possible. It is dependent upon temporal fluctuations in the relative fitness of sexually and asexually produced propagules and/or in sexual versus asexual fecundity. A study of natural populations of the partly asexual plant Allium vineale (wild garlic) revealed that genetic variation for the allocation to sexual and asexual reproduction exists under field conditions. Moreover, considerable fluctuations in the proportions of sexually and asexually produced propagules occurred between years, a state of affairs likely to be instrumental in maintaining a balance between the two reproductive modes. An investigation of genetic variation in A. vineale populations across Europe showed asexual reproduction to be more important for the recruitment of offspring over the short term. Recombination turned out to have played a significant role in introducing new genotypes, but at a rate that may well be lower than one sexually produced offspring per generation. How a balanced reproductive system can be maintained when sexual recruitment occurs at such a low rate is at present unclear. In A. vineale a greenhouse study showed that the genetic correlation between the allocation to sexual and to asexual reproduction differed among sexually and asexually produced offspring. Thus, selecting for an increase in the allocation to one mode of reproduction may give a different response in the allocation to the other mode, depending on whether selection acts among sexually or asexually produced individuals. This may explain why the capacity of sexual reproduction has persisted in this species despite its apparently low 'effective' rate